Many software tools are currently available to solve the hard goal of assembling millions of fragments produced in sequencing projects. Such a variety includes packages for long and short reads, generated by classical and nextgeneration sequencing technologies. Often the result produced by different tools can diverge - sometime significantly - for many reasons: the underlying algorithm, the data structures employed, the heuristics implemented, default parameters, etc. On the ground of the above considerations, we were motivated in developing a methodology which may both guide in a comparison of different assembler’s output and improve the overall quality of the genome assembly sequences, by merging the sequences produced by different assembly programs. © 2009 IEEE.